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The main thing to be aware of is which skills in each perk tree are commonly found on items, entourage and characters - almost all the trees have at least one common particular one (eg. Combustion for engineering, Cooking for Survival, Electromagnets for naturalist, etc) and which are pretty much only available in one place, because THOSE are the hard to get ones.
That said, there are some trees that're definately harder to get a lot of perks in. Archeaology, for example, there's only one item for it at all, and if you don't go to the Celtic starter or Egypt, you aren't going to get any events for them either (and if you've got more naturalist than archeaology, you'll not get it in Egypt either).
However, those trees that are much harder to specialise in are generally powerful in other ways - eg. Tactics for numerous combat bonuses, Archeaology can actually get you an additional treasure in the right place which nothing else will even get a skill roll towards, etc.
I'd say it's about finding which places you really need what for - the world map guides are more of a general hint than anything else, but specialised knowledge or experience will trump the notes anyway; much like Pinkerton's treasure recommendations- once you know better than him, you don't need him anymore, but he can certainly get you started down the right track.
As a general guide, the commoner perks all available in multiple places in the game, and most of them are available on items or else are guarenteed entourages. One or two can be got easily from campfire cards, but those are also character-dependant, so I wouldn't include them as common, as such. I can recommend using the shop guide here: http://steamcommunity.com/sharedfiles/filedetails/?id=544325277 for item listings with the perks, though the RE:IS wiki has a full skill listing which may be more helpful.
Also worth noting that all characters with 2 of the same perk tree have one common and one rare perk of them. Characters that divide them, it varies. Some get 1 rare 1 common, some get two common ones, etc. In general, where a character HAS got a rare perk, that's the one they share when someone admires them.
Also to note - only Engineering and Beguiler have trinkets with 2 perks on 1 item; however, all the engineers/beguilers who start with 2 perks, one of theirs gained through leveling or from the start will be on the item, so it's not quite so easy to stack lots of that perk.
http://renownedexplorers.gamepedia.com/Expeditions